[bio-tools] binding site search utility

[Titus Brown]

Hi all,

I've just written a small program to do a "computational band shift"
against the JASPAR library of t.f. binding sites.  It's available
with a Web interface at:

        http://issola.caltech.edu/~t/slippy-cgi/diff-JASPAR.cgi

The program takes in two oligo sequences -- e.g. a wild-type binding
site that shifts with nuclear extract, and a mutation of that site
that doesn't -- and checks both of them against the JASPAR collection.
Those transcription factors that bind to the first sequence better than
to the sequence sequence are reported, along with the ratio of binding
strengths.

It's probably most useful for people who have done gel shifts with
our nuclear extract & have no idea what's binding...

More information about JASPAR is available from the above Web page;
I think it's probably the best collection of sites available.

cheers,
--titus